SMTL ID : 8bb3.1

Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker (conformation #1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

15 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.1: 3 residues within 4Å: Chain A: R.9, T.12, F.79 No protein-ligand interaction detected (PLIP) SCN.2: 4 residues within 4Å: Chain A: H.10, K.11, C.89, E.91 No protein-ligand interaction detected (PLIP) SCN.3: 4 residues within 4Å: Chain A: R.43, F.85, E.86, A.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.43 SCN.7: 1 residues within 4Å: Chain B: E.75 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.75 SCN.9: 6 residues within 4Å: Chain C: Q.22, R.57, N.90, G.93, Q.94, P.95 1 PLIP interactions: 1 interactions with chain C Water bridges: C:G.93 SCN.10: 4 residues within 4Å: Chain C: Y.105, T.106, E.109 Ligands: SCN.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.106 SCN.11: 3 residues within 4Å: Chain C: V.15, S.17, E.19 No protein-ligand interaction detected (PLIP) SCN.12: 6 residues within 4Å: Chain C: R.69, G.76, E.83, P.103, D.146 Ligands: SCN.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.69 SCN.13: 4 residues within 4Å: Chain C: V.36, P.44, P.46, H.74 No protein-ligand interaction detected (PLIP) SCN.14: 2 residues within 4Å: Chain C: K.145, E.148 No protein-ligand interaction detected (PLIP) SCN.18: 5 residues within 4Å: Chain D: R.141, C.150, L.151, K.152, T.153 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.141 SCN.19: 3 residues within 4Å: Chain D: E.138, S.158, D.159 No protein-ligand interaction detected (PLIP) SCN.20: 2 residues within 4Å: Chain D: K.259, Q.276 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.276 Water bridges: D:Q.276 SCN.21: 4 residues within 4Å: Chain D: Y.247, D.289, L.308, E.309 No protein-ligand interaction detected (PLIP) SCN.22: 6 residues within 4Å: Chain D: S.210, N.212, Y.215, F.253, V.255, L.275 No protein-ligand interaction detected (PLIP)

13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 7 residues within 4Å: Chain A: F.4, F.15, T.16, D.17 Chain B: K.18, H.21, T.64 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.64, A:D.17 EDO.5: 6 residues within 4Å: Chain A: R.37, F.79, R.80, A.81, T.84, E.86 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.37, A:R.37, A:A.81, A:T.84, A:E.86 EDO.8: 4 residues within 4Å: Chain A: F.93 Chain B: H.54, S.57, M.61 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.57 EDO.15: 5 residues within 4Å: Chain C: R.31, V.32, D.70, G.72, T.73 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.32, C:G.72, C:T.73 EDO.16: 2 residues within 4Å: Chain C: V.130, S.132 1 PLIP interactions: 1 interactions with chain C Water bridges: C:S.132 EDO.17: 5 residues within 4Å: Chain D: N.21, A.23, K.25, K.318, S.319 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.21, D:K.25 EDO.24: 7 residues within 4Å: Chain D: N.125, Q.127, N.129, L.130, D.169, G.170, T.187 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.125, D:Q.127 EDO.25: 6 residues within 4Å: Chain D: L.130, I.142, L.151, K.152, T.187, A.188 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.152 EDO.26: 8 residues within 4Å: Chain D: P.42, W.82, S.83, S.84, F.124, N.125, P.126 Ligands: EDO.28 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.83 Water bridges: D:W.82, D:F.124, D:F.124, D:H.165 EDO.27: 2 residues within 4Å: Chain D: C.192, L.193 1 PLIP interactions: 1 interactions with chain D Water bridges: D:Q.191 EDO.28: 4 residues within 4Å: Chain D: N.123, H.165, K.208 Ligands: EDO.26 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.123, D:K.208 EDO.29: 6 residues within 4Å: Chain D: E.45, W.46, G.60, A.61, Y.62, D.63 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.62, D:D.63 EDO.30: 6 residues within 4Å: Chain D: F.253, S.254, V.255, T.256, C.296, H.297 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:V.255, D:T.256 Water bridges: D:F.253, D:F.253

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.6: 10 residues within 4Å: Chain B: M.31, F.48, R.49, E.50, I.51, P.52, E.88, M.91, A.92, F.95 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.49, B:R.49, B:E.50, B:I.51

1 x Q3X: ~{N}-[5-[4-[2-[2-[2-[2-[3-[[3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-3-oxidanylidene-propoxy]ethoxy]ethoxy]ethoxy]ethylcarbamoyl]phenyl]-2-(4-methylpiperazin-1-yl)phenyl]-6-oxidanylidene-4-(trifluoromethyl)-3~{H}-pyridine-3-carboxamide(Non-covalent)

Q3X.23: 31 residues within 4Å: Chain C: N.16, R.18, F.25, P.35, W.37, F.40, Y.47, P.48, R.56, I.58, H.59, S.60, Y.61, H.64, W.66 Chain D: S.36, S.37, A.52, G.76, I.77, S.78, D.79, D.94, F.120, P.160, S.162, Y.178, P.203, C.248, I.292, L.308 25 PLIP interactions: 14 interactions with chain C, 11 interactions with chain D Hydrophobic interactions: C:W.37, C:Y.47, C:I.58, C:I.58, C:Y.61, C:W.66, D:F.120, D:F.120, D:F.120, D:P.160, D:Y.178 Hydrogen bonds: C:R.56, C:H.59, C:S.60, C:Y.61, C:H.64, D:S.78 Water bridges: C:H.59, C:H.59, D:G.76, D:Y.178, D:Y.178 pi-Stacking: C:Y.47, D:F.120 Salt bridges: D:D.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kraemer, A. et al., Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker (conformation #1). To Be Published

Release Date

2022-11-09

Peptides

Elongin-B: A
Elongin-C: B
von Hippel-Lindau disease tumor suppressor: C
WD repeat-containing protein 5: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

B
K

C
L

D
B

Elongin-B

Elongin-C

von Hippel-Lindau disease tumor suppressor

WD repeat-containing protein 5

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